This months edition of Bio::Blogs is now available at Duncan's blog and it is mostly focused on (bio)engineering. Click the link for a summary of interesting things that were blogged about in the past month.
I will be hosting issue number 20 here in the blog, without a clear topic. Possibly with some emphasis on data integration. Email your top picks of the month until the end of March to bioblogs at gmail .com
Showing posts with label Bio::Blogs. Show all posts
Showing posts with label Bio::Blogs. Show all posts
Saturday, March 08, 2008
Friday, February 22, 2008
Call for Bio::Blogs#19
Duncan Hull has volunteer to host the next issue of Bio::Blogs (a bioinformatic related monthly blog journal). It will be out in the beginning of March on the O'Really? blog. The suggested theme for this month is the relationship between Biology and Engineering inspired on the interview published on Edge.org "Engineering and Biology": A Talk with Drew Endy. Anyone can send links for this issue on this topic but also for other interesting bioinformatic posts to bioblogs at gmail.com
We could also try to format if automatically using FeedJournal as suggested by Neil.
We could also try to format if automatically using FeedJournal as suggested by Neil.
Saturday, January 26, 2008
Submissions for Bio::Blogs#18
I am slowly re-connecting to the online world again, trying to pick trough the thousands of blog posts and other RSS feed alerts piled up in GReader. Way before I manage to do that (unless I press the read all button) the next edition of Bio::Blogs will be up at Bioinformatics Zen. Michael Barton has kindly agree to host the 18th edition of Bio::Blogs with a particular emphasis on Open Science and Open Notebook Science. It is scheduled for February 1st and anyone can participate by sending a link of their submissions to bioblogs at gmail.com.
To get in the spirit of the upcoming edition and to inspire some related blog posts go check out his recent movie. What do you think ? Will there be a significant increase of people sharing and collaborating online this year ?
To get in the spirit of the upcoming edition and to inspire some related blog posts go check out his recent movie. What do you think ? Will there be a significant increase of people sharing and collaborating online this year ?
Sunday, December 02, 2007
Merry Bio::Blogs everyone
Paulo Nuin hosted the 17th edition of Bio::Blogs. The number of submissions was very low so I suspect I am not the only one rushing to finish everything before going on holidays.
Should we skip the edition of the 1st of January or maybe postpone it for a few days ? Anyone interested in hosting ? I have been thinking of changing the format a little bit to try to increase the incentives for participating but I'll leave this for another post.
Should we skip the edition of the 1st of January or maybe postpone it for a few days ? Anyone interested in hosting ? I have been thinking of changing the format a little bit to try to increase the incentives for participating but I'll leave this for another post.
Tuesday, November 27, 2007
Bio::Blogs #17 - call for submissions
The 17th edition of Bio::Blogs will be hosted by Paulo Nuin at Blind.Scientist . Submissions of interesting bioinformatic related blog posts of this month can be sent, until the end of the November, to the usual address (bioblogs at gmail dot com) or to nuin at genedrift dot org.
There is also still time to submit blog posts to the OpenLab 2007 compilation.
There is also still time to submit blog posts to the OpenLab 2007 compilation.
Tuesday, November 13, 2007
Last call for Open Laboratory 2007
Bora has issued a last call for submissions to the Science Blogging anthology of 2007. As last year, the objective is to collect some of the best science blog posts of the year and compile it into a book to print on demand (deadline on December 20th 2007). Submissions can be sent using an online form and they will be reviewed by a panel that will compile the final list.Anyone interested in participating can send in links to their favorite blog posts of the year and also volunteer to be part of the reviewing process (see instructions here).
Thursday, November 01, 2007
Bio::Blogs #16, The one with a Halloween theme
The 16# edition of Bio::Blogs is know available at Freelancing science. Jump over there for summary of what has been going on during this month in the bioinformatic related blogs. If not for anything else then just to have a look at the pumpkin. Thanks again to everyone that participated.
Paulo Nuin from Blind.Scientist has volunteered to host the 17# edition that is scheduled to appear as usual on the 1st of December.
Paulo Nuin from Blind.Scientist has volunteered to host the 17# edition that is scheduled to appear as usual on the 1st of December.
Sunday, October 21, 2007
Bio::Blogs #16 - call for submissions
The next edition of Bio::Blogs (bioinformatics blog journal) will be hosted at Freelancing science on the 1st of November. If you find anything this month that you think is interesting to add to this addition send an email to bioblogs at gmail. com until the end of the month. Anyone interested in hosting future edition can also send an email to volunteer.
Wednesday, June 27, 2007
Call for Bio::Blogs #12
I am collecting submissions for the 12th edition of Bio::Blogs. Send in links to blog posts you want to share from your blog or that you enjoyed reading in other blogs to bioblogs at gmail until the end of the month. The next edition will be up at Nodalpoint on the 1st of Jully.
Maybe it could be cool to try out a section on papers of the month as voted by everyone (Neil used to do this once in a while). Anyone interested in participating just has to send a link to a paper, published last month and related to bioinformatics, with a short paragraph explaining what is nice about the paper.
Mike over at Bioinformatics Zen is asking how to continue the Tips and Tricks section of Bio::Blogs. He has put up a wiki page on open science in Nodalpoint to collect information for a possible future edition of the special section.
I am collecting submissions for the 12th edition of Bio::Blogs. Send in links to blog posts you want to share from your blog or that you enjoyed reading in other blogs to bioblogs at gmail until the end of the month. The next edition will be up at Nodalpoint on the 1st of Jully.
Maybe it could be cool to try out a section on papers of the month as voted by everyone (Neil used to do this once in a while). Anyone interested in participating just has to send a link to a paper, published last month and related to bioinformatics, with a short paragraph explaining what is nice about the paper.
Mike over at Bioinformatics Zen is asking how to continue the Tips and Tricks section of Bio::Blogs. He has put up a wiki page on open science in Nodalpoint to collect information for a possible future edition of the special section.
Tuesday, May 29, 2007
Reminder for Bio::Blogs#11
I will start collecting posts for the 11th edition of Bio::Blogs (monthly bioinformatics blog journal) to be hosted at Nodalpoint on the 1st of June. Anyone can participate by sending in submissions to bioblogs at gmail. This month there is going to be a special section dedicated to tips for computational biologists, that will be hosted at Bioinformatics Zen. Something like a separate insight issue :). To participate in the special section email Mike (see post) with your tips or write a post and submit the link to him. It can even be just a couple of sentences. Just think of things that you consider to be important for people working in computational biology and send it in.
I will start collecting posts for the 11th edition of Bio::Blogs (monthly bioinformatics blog journal) to be hosted at Nodalpoint on the 1st of June. Anyone can participate by sending in submissions to bioblogs at gmail. This month there is going to be a special section dedicated to tips for computational biologists, that will be hosted at Bioinformatics Zen. Something like a separate insight issue :). To participate in the special section email Mike (see post) with your tips or write a post and submit the link to him. It can even be just a couple of sentences. Just think of things that you consider to be important for people working in computational biology and send it in.
Wednesday, May 02, 2007
Bio::Blogs #10
The 10th edition of Bio::Blogs, the bioinformatics blog journal has been posted at Nodalpoint. The PDF can be downloaded from Box.net.
The 10th edition of Bio::Blogs, the bioinformatics blog journal has been posted at Nodalpoint. The PDF can be downloaded from Box.net.
Thursday, March 01, 2007
Bio::Blogs #8
Editorial musings
Welcome to the eight edition of the bioinformatics blog journal Bio::Blogs. The archive from previous months can be found at bioblogs.wordpress.com. When this carnival was started, more than eight months ago, it had the primary objective to serve as sort of display for some of the best bioinformatics blog posts on the web and to create incentives for other people to promote their blogs and join in the conversation.
Looking back at the past Bio::Blogs editions I would like to think that we have manage to come with with many interesting posts about bioinformatic conferences, tools and useful computational tips like the DNA analysis series by Sandra Porter (I,II,III,IV,V,VI). Bio::Blogs has also been use to promote tools that have been published in blogs like the Genetic Programming Applet from Pierre and research like the correlation between protein-interaction likelihood and protein age (I and II) that I worked on.
Not everything went as I would hope. The submissions to Bio::Blogs have not picked up as I would expect. Some of this can be explained by poor promotion of my part but it is also due to the small size of the bioinformatics blogging community. In any case I think it is worth maintaining Bio::Blogs up and running for some more time before thinking about stopping this experiment.
In this edition a PDF version of all the posts has been created for anyone interested in downloading, printing and reading some fine posts over coffee or tea. Leave comments or send an email (bioblogs at gmail.com) with your thoughts/ideas for the continuation of this blog journal.I think this printed version also gives a more concrete impression of the potential of blogging for scientific communication.
News and Views
GrrlScientist submitted a report on a recent Science paper describing how moths use their antennae to help them stabilize their flight. Apart from some nasty experiments were they authors removed and glued parts of the antenna the work features some interesting neurophysiology analysis used to characterize the sensitivity of the antennae.
From my blog I picked an entry on network reconstruction. I think the increasing amounts of omics data should be better explored than it currently is and network reconstruction methods are a very good way of achieving this. In this paper, Jason Ernst and colleagues used expression data to reconstruct dynamic transcription regulatory interactions. I will try to continue blogging about the topic in future posts.
Comentaries
PLoS ONE was launched about two months ago and it has produced so far an amazing stream of publications. However the initially proposed goal of generating discussions online to promote post-publication reviews as been lagging. Stew and Alf wrote two commentaries (summited by Greg) regarding the progress of PLoS ONE. They both discuss the current lack of infrastructures to stimulate the online discussions at the PLoS ONE site. Stew goes even further by providing to anyone interested a nice Gresemonkey script to add blog comments to the PLoS ONE papers. I hope Chris Surridge and the rest of the PLoS ONE team start deploying soon some of the tools that they have talked about in their blog. They need to make ONE feel like home, a place were a community of people can discuss their papers.
From Deepak we have a post dedicated to what he dubs EcoInformatics. The importance of using computational methods to analyze ecological changes from the molecules to the ecosystems. The problems range from data access to data management and analysis. The complexity and the different scales of organization (i.e. molecules, environment, ecosystems, disease) make this a very promising field for computational biologists.
From ecological changes we move on to human evolution. Phil tries to introduce the possibility of humanity using technology to improve itself. Having a strong interest myself in synthetic biology and man-machine interfaces I would say that we are still far away from having such control. It is nevertheless useful to discuss the implications of emerging technologies to better prepare for the possible changes.
Reviews and tips
I start this section with a post from a bran-new bioinformatics blog called Bioinformatics Zen. Michael Barton submitted his post on useful tips to get organized as a dry lab scientist. I agree with most of his suggestions. I have try to use slightly fancier methods of organizing my work using project managing tools but I end up returning to a more straightforward folder based approach as well.
Neil Saunders sent in a nice tutorial on building AJAX pages for bioinformatics. It is a very well explained introduction with annotated code. If you were ever interested in learning the basics of AJAX but never invested time in it, here is a good chance to try it.
Editorial musings
Welcome to the eight edition of the bioinformatics blog journal Bio::Blogs. The archive from previous months can be found at bioblogs.wordpress.com. When this carnival was started, more than eight months ago, it had the primary objective to serve as sort of display for some of the best bioinformatics blog posts on the web and to create incentives for other people to promote their blogs and join in the conversation.
Looking back at the past Bio::Blogs editions I would like to think that we have manage to come with with many interesting posts about bioinformatic conferences, tools and useful computational tips like the DNA analysis series by Sandra Porter (I,II,III,IV,V,VI). Bio::Blogs has also been use to promote tools that have been published in blogs like the Genetic Programming Applet from Pierre and research like the correlation between protein-interaction likelihood and protein age (I and II) that I worked on.
Not everything went as I would hope. The submissions to Bio::Blogs have not picked up as I would expect. Some of this can be explained by poor promotion of my part but it is also due to the small size of the bioinformatics blogging community. In any case I think it is worth maintaining Bio::Blogs up and running for some more time before thinking about stopping this experiment.
In this edition a PDF version of all the posts has been created for anyone interested in downloading, printing and reading some fine posts over coffee or tea. Leave comments or send an email (bioblogs at gmail.com) with your thoughts/ideas for the continuation of this blog journal.I think this printed version also gives a more concrete impression of the potential of blogging for scientific communication.
News and Views
GrrlScientist submitted a report on a recent Science paper describing how moths use their antennae to help them stabilize their flight. Apart from some nasty experiments were they authors removed and glued parts of the antenna the work features some interesting neurophysiology analysis used to characterize the sensitivity of the antennae.
From my blog I picked an entry on network reconstruction. I think the increasing amounts of omics data should be better explored than it currently is and network reconstruction methods are a very good way of achieving this. In this paper, Jason Ernst and colleagues used expression data to reconstruct dynamic transcription regulatory interactions. I will try to continue blogging about the topic in future posts.
Comentaries
PLoS ONE was launched about two months ago and it has produced so far an amazing stream of publications. However the initially proposed goal of generating discussions online to promote post-publication reviews as been lagging. Stew and Alf wrote two commentaries (summited by Greg) regarding the progress of PLoS ONE. They both discuss the current lack of infrastructures to stimulate the online discussions at the PLoS ONE site. Stew goes even further by providing to anyone interested a nice Gresemonkey script to add blog comments to the PLoS ONE papers. I hope Chris Surridge and the rest of the PLoS ONE team start deploying soon some of the tools that they have talked about in their blog. They need to make ONE feel like home, a place were a community of people can discuss their papers.
From Deepak we have a post dedicated to what he dubs EcoInformatics. The importance of using computational methods to analyze ecological changes from the molecules to the ecosystems. The problems range from data access to data management and analysis. The complexity and the different scales of organization (i.e. molecules, environment, ecosystems, disease) make this a very promising field for computational biologists.
From ecological changes we move on to human evolution. Phil tries to introduce the possibility of humanity using technology to improve itself. Having a strong interest myself in synthetic biology and man-machine interfaces I would say that we are still far away from having such control. It is nevertheless useful to discuss the implications of emerging technologies to better prepare for the possible changes.
Reviews and tips
I start this section with a post from a bran-new bioinformatics blog called Bioinformatics Zen. Michael Barton submitted his post on useful tips to get organized as a dry lab scientist. I agree with most of his suggestions. I have try to use slightly fancier methods of organizing my work using project managing tools but I end up returning to a more straightforward folder based approach as well.
Neil Saunders sent in a nice tutorial on building AJAX pages for bioinformatics. It is a very well explained introduction with annotated code. If you were ever interested in learning the basics of AJAX but never invested time in it, here is a good chance to try it.
Wednesday, February 28, 2007
Bio::Blogs #8
The eighth edition of Bio::Blogs is coming up soon. It is going to be published here on Public Rambling tomorrow night. I almost forgot that this month is shorter than usual :). There are currently 3 submissions sent in. Pick something from your blogs that is bioinformatic related and sent it in (bioblogs at gmail) or leave the link in the comments. Please also let me know if you mind that I create a PDF file including your submission for offline reading. If you don;t have a blog start one and let me know or just send in a link to something that you particularly liked.
The eighth edition of Bio::Blogs is coming up soon. It is going to be published here on Public Rambling tomorrow night. I almost forgot that this month is shorter than usual :). There are currently 3 submissions sent in. Pick something from your blogs that is bioinformatic related and sent it in (bioblogs at gmail) or leave the link in the comments. Please also let me know if you mind that I create a PDF file including your submission for offline reading. If you don;t have a blog start one and let me know or just send in a link to something that you particularly liked.
Friday, February 02, 2007
Bio::Blogs #7
The February edition of Bio::Blogs was just published in BioHacking. Thanks to Paras for editing it. He highlighted some blogs related to synthetic biology and some of the recent bioinformatics posts from Neil, Sandra and Pierre.
The 8th edition will be coming back here. The participation has been generally going down so Bio::Blogs might, in the near future, morph to something else.
Just to give it a little twist I thought that it could be interesting to add a PDF version of Bio::Blogs (with the permission of the authors of course). So, for the next month entries I will be asking if the authors concede that the blog posts be compiled into a printable document.
Entries can be submitted until the end of February to bioblogs at gmail.
The February edition of Bio::Blogs was just published in BioHacking. Thanks to Paras for editing it. He highlighted some blogs related to synthetic biology and some of the recent bioinformatics posts from Neil, Sandra and Pierre.
The 8th edition will be coming back here. The participation has been generally going down so Bio::Blogs might, in the near future, morph to something else.
Just to give it a little twist I thought that it could be interesting to add a PDF version of Bio::Blogs (with the permission of the authors of course). So, for the next month entries I will be asking if the authors concede that the blog posts be compiled into a printable document.
Entries can be submitted until the end of February to bioblogs at gmail.
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